DISTANCES
Convert multiple alignment data to distance matrix

DISTANCES is a FORTRAN77 program which reads a multiple alignment file in PIR or FASTA format, computes the distance matrix determined by the alignment, and writes that matrix to a file.

Languages:

DISTANCES is available in a FORTRAN77 version and a FORTRAN90 version.

Related Data and Programs:

READ_ALIGN is a FORTRAN90 program which can reformat an alignment file so that it can be examined by DISTANCES.

SPACER is a FORTRAN90 program which can read the distance matrix created by DISTANCES and perform a principal component analysis.

SPACER_DATA_CONVERT is a FORTRAN90 program which can read a multiple sequence alignment file and write out the relevant information into a file in PIR format.

Author:

Des Higgins,
EMBL Data Library

Source Code:

• distances.f, the source code;
• distances.sh, commands to compile and load the source code;

Examples and Tests:

• distances_input.txt, an input file;
• distances_output.txt, the output file.
• alignment.txt, a multiple alignment file to be read by DISTANCES;
• alignment.dist, the distance matrix created by DISTANCES;

List of Routines:

• MAIN is the main program for DISTANCES.
• SETAAMAT
• SETAASCORE
• TOSSGAPS
• CHFEXT changes the extension of a filename.
• DISTMAT calculates a similarity matrix between pairs os sequences.
• READSEQS reads a FASTA or PIR format multiple aligment file.
• GETSTR prompts for a string input.
• GETINT prompts for an integer input.

You can go up one level to the FORTRAN77 source codes.